Cloning of the individual genes that are mutated in the neuronal ceroid lipofuscinoses (NCLs), or Batten disease, has opened up new avenues of research into the pathogenesis of these fatal autosomal recessive storage disorders. Genetically accurate mouse models have now been generated for each major form of the disorder, together with several variant forms. Ongoing analysis of these mice is revealing significant new data about the staging and progression of disease phenotypes. Combined with data from human autopsy tissues and large animal models, it is now clear that neurodegeneration is initially selective in the NCL CNS, targeting specific regions and particular cell populations. There is also evidence of selective glial activation that appears to precede obvious neurodegeneration, becoming more widespread with disease progression. Currently, there is debate over the mechanisms of cell death that operate in each form of NCL, with evidence of both apoptosis and autophagy. It is likely that these mechanisms may encompass a spectrum of cell death events, depending upon the specific context of each neuronal population. Taken together, these data have significant clinical implications for the development and targeting of appropriate therapeutic strategies, and for providing the landmarks to judge their efficacy.